View source: R/normalization.R
estNormFactors | R Documentation |
This function estimates normalization factors for the input 'seqCountSet' object and return the same object with normalizationFactor field filled or replaced.
## S4 method for signature 'SeqCountSet'
estNormFactors(seqData, method=c("lr", "quantile", "total", "median"))
seqData |
An object of "SeqCountSet" class. |
method |
Methods to be used in computing normalization factors. Currently available options only include methods to compute normalization factor to adjust for sequencing depths. Available options use (1) "lr": using median of logratio of counts. Similar to the TMM method. (2) "quantile" (default): 75th quantile, (3) "total": total counts, or (4) "median": median counts to constuct the normalization factors. From all methods the normalization factor will be a vector with same length as number of columns for input counts. |
The same "SeqCountSet" object with normalizationFactor field filled or replaced.
Hao Wu <hao.wu@emory.edu>
data(seqData)
## compare different methods
seqData=estNormFactors(seqData, "lr")
k1=normalizationFactor(seqData)
seqData=estNormFactors(seqData, "quantile")
k2=normalizationFactor(seqData)
seqData=estNormFactors(seqData, "total")
k3=normalizationFactor(seqData)
cor(cbind(k1,k2,k3))
## assign size factor
normalizationFactor(seqData)=k1
## or normalization factor can be a matrix
dd=exprs(seqData)
f=matrix(runif(length(dd), 1,10), nrow=nrow(dd), ncol=ncol(dd))
normalizationFactor(seqData)=f
head(normalizationFactor(seqData))
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